Hi Mehul,
if you set them to white matter hypointensities in the aseg.mgz I think
they will get filled properly.
cheers
Bruce
On Tue, 4 May 2010, Mehul Sampat wrote:
> Hi Folks,
>
> We have some subjects with very large white matter (WM) lesion loads.
> We noticed that the pial and main are pi
Hi Folks,
We have some subjects with very large white matter (WM) lesion loads.
We noticed that the pial and main are pial surfaces are not affected by WM
lesions.
However, they seem to be affection by the juxta-cortical WM lesions (which
have dark intensity)
In the past, my colleagues have manua
it should keep all control points and manual edits
Bruce
On Tue, 4 May 2010, Ilana
Hairston wrote:
> sorry for being dense - but what then would be the best way to acheive
> better wm intensity?
> We get much better contrasts and better segmentation in fronto-temporal
> regions when we run mri_n
Dear freesurfer developers:
As I searched wiki, the freesurfer only provided whole-brain FDR and
cluster simulation for multiple comparison correction. Is there any
way to perform the smell volume correction for the regional cortical
thickness in specific regions as it in SPM?
Thanks for your kin
sorry for being dense - but what then would be the best way to acheive
better wm intensity?
We get much better contrasts and better segmentation in fronto-temporal
regions when we run mri_nu_correct.mni. But then we still need to fix
topological errors. My understanding is that '-make all' fixes
Hi Ilana
that won't work. I guess you could try copying nu2.mgz to nu.mgz and
trying -make all (assuming you have a new enough version of recon-all)
cheers
Bruce
On
Tue, 4 May 2010, Ilana Hairston wrote:
> Also re-sending my query - perhaps someone has experience with contrast
> adjustments
>
Hello Doug-
When using mri_mcsim, is there an option to reduce the iterations of
fwhm values? I'd like to create a database of sims within an in-house
average subject as well as within different labels, but I have no need
for 30 fwhm values. If I could restrict it to just a few choice values,
yes, but if the information is lost in analyze (which it is) then we are
just guessing about orientations when we are converting back to .mgz
On Tue,
4 May 2010, Ilana Hairston wrote:
trying to make sense of this:
1. ran the initial recon-all to convert analyze to .mgz
2. then mri_convert on
Also re-sending my query - perhaps someone has experience with contrast
adjustments
We have been doing contrast correction using mri_nu_correct.mni after
> autorecon-all
>
(e.g.,
>
mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o
> FS090620ll/mri/orig/nu2.mgz --n 2).
>
> My question is w
Hi all,
I have a set of 32 labels that I am attempting to pull average thickness from.
I would prefer not to run 32 different asegstats2table commands, so I was
wondering if there was any way to consolidate the thickness stats from these
labels into one file so I can pull them all out simultan
Dear All,
I am new to freesurfer, in some of our patients stats files lh and
rh.curv.stats are missing at the end of recon-all -all. recon-all finished
without error in these patients so i am wondering what is the mistake i am
doing and where will need these lh and rh.curv stats files.
Thanks
If you don't have MatLAB, you can also do:
$>mris_calc -out lh.thickness.asc lh.thickness ascii
which will convert the 'lh.thickness' into an ascii file (in this case,
'lh.thickness.asc') containing the thickness per vertex per line.
Incidentally, this will work with any FreeSurfer curvature fi
trying to make sense of this:
1. ran the initial recon-all to convert analyze to .mgz
2. then mri_convert on the DICOMs overwriting 001.mgz.
Now running the full autorecon-all to see what it looks like, but is seems
that mri_convert added spatial cosine information to the 001.mgz. this was
the o
you actually don't need to set it to anything if you give it an output
file with a format extention. Eg, out.mgh
doug
Ritobrato Datta wrote:
> Hello All,
>
> I posted this question yesterday. It probably got lost. So I am posting
> again.
>
> For functional data to be resampled to fsaverage us
usually you create an mri/orig/001.mgz, but you can also just point
recon-all directly at the dicoms I think
On Tue, 4 May 2010, Antoine Leflon
wrote:
So I have to write : mri_convert -it dicom -i (first image) -o (name
of the file) ?
I did it outputing orig.mgz as usually before getting the e
So I have to write : mri_convert -it dicom -i (first image) -o (name
of the file) ?
I did it outputing orig.mgz as usually before getting the error .
Antoine
Bruce Fischl a écrit :
> mri_convert can be used to ch
there's a tutorial for this on the wiki. It's pretty detailed - let us
know if you have any problems.
cheers
Bruce
On Tue, 4 May 2010, Antoine Leflon wrote:
No I haven't , what is the syntax for this ?
tkregister2 (name) (mgz file) ?
thanks ,
Antoine
No I haven't , what is the syntax for this ?
tkregister2 (name) (mgz file) ?
thanks ,
Antoine
Bruce Fischl a écrit :
> have you visually verified the talairach failed with tkregister2? If you
> bring up the orig.m
if the directions are labeled properly then you aer probably ok. In
general you are better off just giving recon-all the dicom files as input
and not doing any conversions beforehand.
cheers
Bruce
On Tue, 4 May 2010,
chenchunhuichina wrote:
Hello FreeSurfer users,
I may be asking a stupid
mri_convert can be used to change the format, assuming it is standard
dicom.
cheers
Bruce
On Tue, 4 May 2010, Antoine Leflon wrote:
> My files are dicoms and have no extension in the end of their name
> (IM_0465 for example) . Is it possible to change the format ?
>
> thanks ,
>
> Antoine
>
>
>
have you visually verified the talairach failed with tkregister2? If you
bring up the orig.mgz does it show properly (that is, is the view it calls
coronal actually coronal, etc...)?
On Tue, 4
May 2010, Antoine Leflon wrote:
> Hi all ,
>
> I've used data from another Doctor , freesurfer told m
Hi Ri,
what format is your functional data in? How did you analyze it?
Bruce
On Tue, 4
May 2010, Ritobrato Datta wrote:
> Hello All,
>
> I posted this question yesterday. It probably got lost. So I am posting again.
>
> For functional data to be resampled to fsaverage using mri_surf2surf what
Hello All,
I posted this question yesterday. It probably got lost. So I am posting again.
For functional data to be resampled to fsaverage using mri_surf2surf what
should be used with " --sfmt " flag ?
For the thickness the --sfmt curv is used when running qcache.
Thanks
Ri
Hi Ana,
yes, it's stored in the ?h.thickness file, which you can load into matlab
or tksurfer for visualization/analysis.
cheers
Bruce
On Tue, 4 May 2010, Ana Catarino
wrote:
> Hello,
>
> Does anyone know if there is a way of getting access to the values of
> thickness for each voxel / point i
*Use the commands:*
*mri_surf2surf --s subject --hemi lh --sval-tal-xyz white **--tval-xyz
--tval lh.white.tal**
*
*mris_convert lh.white.tal lh.white.tal.asc*
Ref:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011618.html
You can make search in previous answers of the ma
Hello,
Does anyone know if there is a way of getting access to the values of
thickness for each vertex in the mesh?
Thank you,
Ana Catarino
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My files are dicoms and have no extension in the end of their name
(IM_0465 for example) . Is it possible to change the format ?
thanks ,
Antoine
Talairach is about orientation. What is the format of your file?
Hi all ,
I've used data from another Doctor , freesurfer told me the FOV was
330 so I put the flag -cw256 in the command recon-all but the
Talairach just failed ...
I got this error message . Can someone explain please ?
_
hello all ,
I managed to run recon-all fully and I got a table with the following colums :
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
Hello,
Does anyone know if there is a way of getting access to the values of
thickness for each voxel / point in the mesh?
Thank you,
Ana Catarino
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Hello FreeSurfer users,
I may be asking a stupid question but it really troubled me a while.
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it
displayed in RAS coordinates, but template of FSL are in LAS coordinates.
Should I filp L-R before doing any further analysis?
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